Plasmid-driven strategies for clone success in Escherichia coli
Escherichia coli is the most widely studied microbe in history, but the population structure and evolutionary trends of its extrachromosomal elements known as plasmids remain poorly delineated. Here we used long-read technology to high-resolution sequence the entire plasmidome and the corresponding host chromosomes from an unbiased longitudinal survey covering two decades and over 2000 E. coli isolates. We find that some plasmids have persisted in lineages even for centuries, demonstrating strong plasmid-lineage associations. Our analysis provides a detailed map of recent vertical and horizontal evolutionary events involving plasmids with key antibiotic resistance, competition and virulence determinants. We present genomic evidence of both chromosomal and plasmid-driven success strategies adopted by distant lineages by independently inheriting the same genomic elements. Further, we use in vitro experiments to verify the importance of key bacteriocin-producing plasmids for clone success. Our study has general implications for understanding plasmid biology and bacterial evolutionary strategies.
Authors
- Sergio Arredondo-Alonso (ORCID: https://orcid.org/0000-0002-4445-2442)
- Anna Kaarina Pöntinen (ORCID: https://orcid.org/0000-0002-3160-2042)
- Jukka Corander (ORCID: https://orcid.org/0000-0002-7752-1942)
- Gerry Q. Tonkin‐Hill (ORCID: https://orcid.org/0000-0003-4397-2224)
- Gunnar Skov Simonsen (ORCID: https://orcid.org/0000-0003-0043-7045)
- Harry A. Thorpe (ORCID: https://orcid.org/0000-0001-5895-3232)
- Ørjan Samuelsen (ORCID: https://orcid.org/0000-0002-5525-2614)
- João Alves Gama (ORCID: https://orcid.org/0000-0003-0967-6616)
- Rebecca Ashley Gladstone (ORCID: https://orcid.org/0000-0002-7993-3051)
- Klaus Harms (ORCID: https://orcid.org/0000-0003-1454-0692)
- Pål J. Johnsen (ORCID: https://orcid.org/0000-0002-6455-6433)
Institutions
- University Hospital of North Norway (NO)
- The University of Melbourne (AU)
- University of Oslo (NO)
- Instituto Cajal (ES)
- Peter MacCallum Cancer Centre (AU)
- Wellcome Sanger Institute (GB)
- Helsinki Institute for Information Technology (FI)
- Peter Doherty Institute (AU)
- Instituto Ramón y Cajal de Investigación Sanitaria (ES)
- UiT The Arctic University of Norway (NO)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-04-03
- DOI
- https://doi.org/10.1038/s41467-025-57940-1
- Citations
- 24
- Primary Topic
- Antibiotic Resistance in Bacteria
- Type
- article
- Field-Weighted Citation Impact
- 13.01